Last updated: 2020-08-04
Checks: 7 0
Knit directory: Embryoid_Body_Pilot_Workflowr/
This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.
Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.
The command set.seed(20200804) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.
Great job! Recording the operating system, R version, and package versions is critical for reproducibility.
Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.
Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
The results in this page were generated with repository version 422197b. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.
Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
Ignored files:
Ignored: .Rhistory
Ignored: .Rproj.user/
Untracked files:
Untracked: analysis/child/
Unstaged changes:
Modified: .Rprofile
Modified: .gitattributes
Modified: .gitignore
Modified: Embryoid_Body_Pilot_Workflowr.Rproj
Modified: README.md
Modified: _workflowr.yml
Modified: analysis/_site.yml
Modified: analysis/about.Rmd
Modified: analysis/index.Rmd
Modified: analysis/license.Rmd
Modified: code/README.md
Modified: data/README.md
Modified: output/README.md
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
These are the previous versions of the repository in which changes were made to the R Markdown (analysis/SampleFilteringandSCT_Batch1Lane1.Rmd) and HTML (docs/SampleFilteringandSCT_Batch1Lane1.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 422197b | KLRhodes | 2020-08-04 | testing knit expand |
library(knitr)
library(Seurat)
library(Matrix)
library(DropletUtils)Loading required package: SingleCellExperimentLoading required package: SummarizedExperimentLoading required package: GenomicRangesLoading required package: stats4Loading required package: BiocGenericsLoading required package: parallel
Attaching package: 'BiocGenerics'The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLBThe following object is masked from 'package:Matrix':
whichThe following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabsThe following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.minLoading required package: S4Vectors
Attaching package: 'S4Vectors'The following object is masked from 'package:Matrix':
expandThe following object is masked from 'package:base':
expand.gridLoading required package: IRangesLoading required package: GenomeInfoDbLoading required package: BiobaseWelcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.Loading required package: DelayedArrayLoading required package: matrixStats
Attaching package: 'matrixStats'The following objects are masked from 'package:Biobase':
anyMissing, rowMediansLoading required package: BiocParallel
Attaching package: 'DelayedArray'The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRangesThe following objects are masked from 'package:base':
aperm, apply, rowsum
Attaching package: 'SummarizedExperiment'The following object is masked from 'package:Seurat':
Assayslibrary(ggplot2)
library(dplyr)
Attaching package: 'dplyr'The following object is masked from 'package:matrixStats':
countThe following object is masked from 'package:Biobase':
combineThe following objects are masked from 'package:GenomicRanges':
intersect, setdiff, unionThe following object is masked from 'package:GenomeInfoDb':
intersectThe following objects are masked from 'package:IRanges':
collapse, desc, intersect, setdiff, slice, unionThe following objects are masked from 'package:S4Vectors':
first, intersect, rename, setdiff, setequal, unionThe following objects are masked from 'package:BiocGenerics':
combine, intersect, setdiff, unionThe following objects are masked from 'package:stats':
filter, lagThe following objects are masked from 'package:base':
intersect, setdiff, setequal, unionlibrary(here)here() starts at /project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowrload rds
samp.obj<- readRDS('/project2/gilad/katie/Pilot_HumanEBs/HumanEB_QCmetadata/Batch1_Lane1_seurat_NoNorm_QCMetaAdded.rds')qc<- knitr::knit_expand(file = here::here("analysis/child/SampleFilteringAndSCT.Rmd"))knitr::knit(text=unlist(qc))
sessionInfo()R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)
Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so
locale:
[1] C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] here_0.1-11 dplyr_1.0.0
[3] ggplot2_3.3.2 DropletUtils_1.6.1
[5] SingleCellExperiment_1.8.0 SummarizedExperiment_1.16.1
[7] DelayedArray_0.12.3 BiocParallel_1.20.1
[9] matrixStats_0.56.0 Biobase_2.46.0
[11] GenomicRanges_1.38.0 GenomeInfoDb_1.22.1
[13] IRanges_2.20.2 S4Vectors_0.24.4
[15] BiocGenerics_0.32.0 Matrix_1.2-18
[17] Seurat_3.2.0 knitr_1.29
[19] workflowr_1.6.2
loaded via a namespace (and not attached):
[1] backports_1.1.8 plyr_1.8.6 igraph_1.2.5
[4] lazyeval_0.2.2 splines_3.6.1 listenv_0.8.0
[7] digest_0.6.25 htmltools_0.5.0 gdata_2.18.0
[10] magrittr_1.5 tensor_1.5 cluster_2.1.0
[13] ROCR_1.0-7 limma_3.42.2 globals_0.12.5
[16] R.utils_2.9.2 colorspace_1.4-1 rappdirs_0.3.1
[19] ggrepel_0.8.2 xfun_0.16 crayon_1.3.4
[22] RCurl_1.98-1.2 jsonlite_1.7.0 spatstat_1.64-1
[25] spatstat.data_1.4-3 survival_3.2-3 zoo_1.8-8
[28] ape_5.3 glue_1.4.1 polyclip_1.10-0
[31] gtable_0.3.0 zlibbioc_1.32.0 XVector_0.26.0
[34] leiden_0.3.3 Rhdf5lib_1.8.0 future.apply_1.6.0
[37] HDF5Array_1.14.4 abind_1.4-5 scales_1.1.1
[40] edgeR_3.28.1 miniUI_0.1.1.1 Rcpp_1.0.5
[43] viridisLite_0.3.0 xtable_1.8-4 dqrng_0.2.1
[46] reticulate_1.16 rsvd_1.0.3 htmlwidgets_1.5.1
[49] httr_1.4.2 gplots_3.0.4 RColorBrewer_1.1-2
[52] ellipsis_0.3.1 ica_1.0-2 pkgconfig_2.0.3
[55] R.methodsS3_1.8.0 uwot_0.1.8 deldir_0.1-28
[58] locfit_1.5-9.4 tidyselect_1.1.0 rlang_0.4.7
[61] reshape2_1.4.4 later_1.1.0.1 munsell_0.5.0
[64] tools_3.6.1 generics_0.0.2 ggridges_0.5.2
[67] evaluate_0.14 stringr_1.4.0 fastmap_1.0.1
[70] yaml_2.2.1 goftest_1.2-2 npsurv_0.4-0
[73] fs_1.4.2 fitdistrplus_1.0-14 caTools_1.18.0
[76] purrr_0.3.4 RANN_2.6.1 pbapply_1.4-2
[79] future_1.18.0 nlme_3.1-140 whisker_0.4
[82] mime_0.9 R.oo_1.23.0 compiler_3.6.1
[85] plotly_4.9.2.1 png_0.1-7 lsei_1.2-0
[88] spatstat.utils_1.17-0 tibble_3.0.3 stringi_1.4.6
[91] lattice_0.20-38 vctrs_0.3.2 pillar_1.4.6
[94] lifecycle_0.2.0 lmtest_0.9-37 RcppAnnoy_0.0.16
[97] data.table_1.13.0 cowplot_1.0.0 bitops_1.0-6
[100] irlba_2.3.3 httpuv_1.5.4 patchwork_1.0.1
[103] R6_2.4.1 promises_1.1.1 KernSmooth_2.23-15
[106] gridExtra_2.3 codetools_0.2-16 MASS_7.3-51.4
[109] gtools_3.8.2 rhdf5_2.30.1 rprojroot_1.3-2
[112] withr_2.2.0 sctransform_0.2.1 GenomeInfoDbData_1.2.2
[115] mgcv_1.8-28 grid_3.6.1 rpart_4.1-15
[118] tidyr_1.1.0 rmarkdown_2.3 Rtsne_0.15
[121] git2r_0.26.1 shiny_1.5.0